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In rEEMSplots, add a function
eems.posterior.draws to draw and plot…
… samples from the posterior.
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| *.png | ||
| *.so | ||
| *.o | ||
| .Rproj.user | ||
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| ^.*\.Rproj$ | ||
| ^\.Rproj\.user$ |
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| library(rEEMSplots) | ||
| library(rEEMSplots) | ||
| library(rEEMSplots) | ||
| ?eems.voronoi | ||
| ## Use the provided example or supply the path to your own EEMS run. | ||
| eems.results.to.plot = paste(path.package("rEEMSplots"),"/extdata/EEMS-example",sep="") | ||
| name.figures.to.save= "EEMS-example-rEEMSplots" | ||
| path.expand("~") | ||
| ?path.expand | ||
| path.expand("~/"EEMS-example-rEEMSplots"") | ||
| path.expand("~/"EEMS-example-rEEMSplots") | ||
| path.expand("~/EEMS-example-rEEMSplots") | ||
| ## Use the provided example or supply the path to your own EEMS run. | ||
| eems.results.to.plot = paste(path.package("rEEMSplots"),"/extdata/EEMS-example",sep="") | ||
| name.figures.to.save= "EEMS-example-rEEMSplots" | ||
| library(deldir) | ||
| ## Plot a series of Voronoi diagrams for the EEMS model parameters: | ||
| ## the effective migration rates (m) and the effective diversity rates (q). | ||
| eems.voronoi(mcmcpath = eems.results.to.plot, | ||
| plotpath = paste(name.figures.to.save,"-voronoi-diagrams",sep=""), | ||
| longlat = TRUE,mcmc.iters = seq(9)) | ||
| library("rworldmap") | ||
| library("rworldxtra") | ||
| install.packages("rworldmap") | ||
| remove.packages("spam") | ||
| install.packages("spam") | ||
| ?image | ||
| ?plot | ||
| library(spam) | ||
| install.packages("rworldmap") | ||
| remove.packages("fields") | ||
| install.packages("fields") | ||
| install.packages("rworldmap") | ||
| library("rgdal") | ||
| library("rworldmap") | ||
| library("rworldxtra") | ||
| library("RColorBrewer") | ||
| library("deldir") | ||
| library(rEEMSplots) | ||
| ?eems.voronoi | ||
| ?eems.plots | ||
| x = letters | ||
| sample(letters, 1) | ||
| sample(letters, 1) | ||
| sample(letters, 1) | ||
| sample(letters, 1) | ||
| sample(letters, 1) | ||
| sample(letters, 1) | ||
| sample(letters, 1) | ||
| sample(letters, 1) | ||
| sample(letters, 1) | ||
| samples(seq(20), 1) | ||
| sample(seq(20), 1) | ||
| sample(seq(20), 1) | ||
| tiles = 1:12 | ||
| iter = 3 | ||
| sum(tiles[1:(iter-1)]) | ||
| sum(tiles[iter:1]) | ||
| sum(tiles[iter:1][-1]) | ||
| iter = 1 | ||
| sum(tiles[iter:1][-1]) | ||
| sum(tiles[iter:1][-1]) | ||
| library(rEEMSplots) | ||
| library(rEEMSplots) | ||
| library(rEEMSplots) | ||
| ?eems.voronoi | ||
| library(rEEMSplots) | ||
| ?eems.voronoi | ||
| eems.results.to.plot = paste0(path.package("rEEMSplots"), "/extdata/EEMS-example", sep = "") | ||
| name.figures.to.save = path.expand("~/EEMS-example-rEEMSplots") | ||
| library("deldir") | ||
| eems.voronoi(mcmcpath = eems.results.to.plot, | ||
| plotpath = paste0(name.figures.to.save, "-voronoi-diagrams"), | ||
| longlat = TRUE, post.draws = 10) | ||
| ?bitmap | ||
| library(grDevices) | ||
| eems.voronoi(mcmcpath = eems.results.to.plot, | ||
| plotpath = paste0(name.figures.to.save, "-voronoi-diagrams"), | ||
| longlat = TRUE, post.draws = 10) | ||
| library(graphics) | ||
| eems.voronoi(mcmcpath = eems.results.to.plot, | ||
| plotpath = paste0(name.figures.to.save, "-voronoi-diagrams"), | ||
| longlat = TRUE, post.draws = 10) | ||
| ?plot.new | ||
| ?.filled.contour | ||
| library(rEEMSplots) | ||
| ?mtext | ||
| ?bitmap | ||
| library(rEEMSplots) | ||
| library(rEEMSplots) | ||
| library(rEEMSplots) | ||
| ?image | ||
| ?bitmap | ||
| library(rEEMSplots) | ||
| ?par | ||
| ?layout | ||
| ?lcm | ||
| library(rEEMSplots) | ||
| ?devv.off | ||
| ?dev.off | ||
| ?col2rgb | ||
| library(rEEMSplots) | ||
| ?eems.voronoi | ||
| ## Use the provided example or supply the path to your own EEMS run. | ||
| eems.results.to.plot = paste0(path.package("rEEMSplots"), "/extdata/EEMS-example", sep = "") | ||
| name.figures.to.save = path.expand("~/EEMS-example-rEEMSplots") | ||
| library("deldir") | ||
| ## Plot a series of Voronoi diagrams for the EEMS model parameters: | ||
| ## the effective migration rates (m) and the effective diversity rates (q). | ||
| eems.voronoi(mcmcpath = eems.results.to.plot, | ||
| plotpath = paste0(name.figures.to.save, "-voronoi-diagrams"), | ||
| longlat = TRUE, post.draws = 10) | ||
| library(rEEMSplots) | ||
| library(rEEMSplots) | ||
| ## Use the provided example or supply the path to your own EEMS run. | ||
| eems.results.to.plot = paste0(path.package("rEEMSplots"), "/extdata/EEMS-example", sep = "") | ||
| name.figures.to.save = path.expand("~/EEMS-example-rEEMSplots") | ||
| library("deldir") | ||
| ## Plot a series of Voronoi diagrams for the EEMS model parameters: | ||
| ## the effective migration rates (m) and the effective diversity rates (q). | ||
| eems.voronoi(mcmcpath = eems.results.to.plot, | ||
| plotpath = paste0(name.figures.to.save, "-voronoi-diagrams"), | ||
| longlat = TRUE, post.draws = 10) | ||
| ?eems.popgrid | ||
| path.expand("~/EEMS-barrier") | ||
| ?eems.voronoi | ||
| ?stopifnot | ||
| ?nlevels | ||
| library(rEEMSplots) | ||
| library(rEEMSplots) | ||
| library(rEEMSplots) | ||
| ?random.eems.draws | ||
| ?eems.posterior.draws | ||
| ## Use the provided example or supply the path to your own EEMS run. | ||
| eems.results.to.plot = paste0(path.package("rEEMSplots"), "/extdata/EEMS-example", sep = "") | ||
| name.figures.to.save = path.expand("~/EEMS-example-rEEMSplots") | ||
| ## Plot a series of Voronoi diagrams for the EEMS model parameters: | ||
| ## the effective migration rates (m) and the effective diversity rates (q). | ||
| eems.posterior.draws(mcmcpath = eems.results.to.plot, | ||
| plotpath = paste0(name.figures.to.save, "-posterior-draws"), | ||
| longlat = TRUE, post.draws = 10) | ||
| library(rEEMSplots) | ||
| ## Use the provided example or supply the path to your own EEMS run. | ||
| eems.results.to.plot = paste0(path.package("rEEMSplots"), "/extdata/EEMS-example", sep = "") | ||
| name.figures.to.save = path.expand("~/EEMS-example-rEEMSplots") | ||
| ## Plot a series of Voronoi diagrams for the EEMS model parameters: | ||
| ## the effective migration rates (m) and the effective diversity rates (q). | ||
| eems.posterior.draws(mcmcpath = eems.results.to.plot, | ||
| plotpath = paste0(name.figures.to.save, "-posterior-draws"), | ||
| longlat = TRUE, post.draws = 10) | ||
| library(rEEMSplots) | ||
| library(rEEMSplots) | ||
| ?eems.voronoi | ||
| ## Use the provided example or supply the path to your own EEMS run. | ||
| eems.results.to.plot = paste0(path.package("rEEMSplots"), "/extdata/EEMS-example", sep = "") | ||
| name.figures.to.save = path.expand("~/EEMS-example-rEEMSplots") | ||
| library("deldir") | ||
| ## Plot a series of Voronoi diagrams for the EEMS model parameters: | ||
| ## the effective migration rates (m) and the effective diversity rates (q). | ||
| eems.voronoi(mcmcpath = eems.results.to.plot, | ||
| plotpath = paste0(name.figures.to.save, "-voronoi-diagrams"), | ||
| longlat = TRUE, post.draws = 10) | ||
| library(rEEMSplots) | ||
| ## Use the provided example or supply the path to your own EEMS run. | ||
| eems.results.to.plot = paste0(path.package("rEEMSplots"), "/extdata/EEMS-example", sep = "") | ||
| name.figures.to.save = path.expand("~/EEMS-example-rEEMSplots") | ||
| library("deldir") | ||
| ## Plot a series of Voronoi diagrams for the EEMS model parameters: | ||
| ## the effective migration rates (m) and the effective diversity rates (q). | ||
| eems.voronoi(mcmcpath = eems.results.to.plot, | ||
| plotpath = paste0(name.figures.to.save, "-voronoi-diagrams"), | ||
| longlat = TRUE, post.draws = 10) | ||
| ?eems.voronoi | ||
| q() |
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| # Generated by roxygen2: do not edit by hand | ||
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| export(eems.plots) | ||
| export(eems.popgrid) | ||
| export(eems.posterior.draws) | ||
| export(eems.resid.heatmap) | ||
| export(eems.voronoi) | ||
| export(eems.popgrid) | ||
| import(Rcpp) | ||
| import(RcppEigen) | ||
| import(geosphere) | ||
| import(raster) | ||
| import(rgeos) | ||
| import(sp) | ||
| importFrom(Rcpp,evalCpp) | ||
| importFrom(grDevices,bitmap) | ||
| importFrom(grDevices,col2rgb) | ||
| importFrom(grDevices,colorRampPalette) | ||
| importFrom(grDevices,dev.off) | ||
| importFrom(grDevices,pdf) | ||
| importFrom(graphics,.filled.contour) | ||
| importFrom(graphics,Axis) | ||
| importFrom(graphics,abline) | ||
| importFrom(graphics,axis) | ||
| importFrom(graphics,box) | ||
| importFrom(graphics,layout) | ||
| importFrom(graphics,lcm) | ||
| importFrom(graphics,legend) | ||
| importFrom(graphics,mtext) | ||
| importFrom(graphics,par) | ||
| importFrom(graphics,plot.new) | ||
| importFrom(graphics,plot.window) | ||
| importFrom(graphics,points) | ||
| importFrom(graphics,polygon) | ||
| importFrom(graphics,rect) | ||
| importFrom(graphics,title) | ||
| useDynLib(rEEMSplots) |
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| # This file was generated by Rcpp::compileAttributes | ||
| # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393 | ||
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| resistance_distance <- function(M) { | ||
| .Call('rEEMSplots_resistance_distance', PACKAGE = 'rEEMSplots', M) | ||
| } | ||
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| rcppstandardize_rates <- function(tiles, rates, seeds, marks, distm) { | ||
| .Call('rEEMSplots_rcppstandardize_rates', PACKAGE = 'rEEMSplots', tiles, rates, seeds, marks, distm) | ||
| } | ||
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| rcppdont_standardize_rates <- function(tiles, rates, seeds, marks, distm) { | ||
| .Call('rEEMSplots_rcppdont_standardize_rates', PACKAGE = 'rEEMSplots', tiles, rates, seeds, marks, distm) | ||
| } | ||
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